Contacts of the helix formed by residues 15 - 24 (chain D) in PDB entry 4N3E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D PRO 3.9 0.2 + - - -
14D ILE* 1.3 78.6 - - - +
16D PRO* 1.4 76.0 - - + +
17D HIS* 2.9 18.6 + - + -
18D ARG* 3.0 20.0 + - + +
19D LEU* 3.2 6.9 + - - +
110D GLY 3.7 11.8 + - - +
111D GLY* 4.1 0.7 - - - -
17X HIS* 3.2 37.7 - - + +
159X ALA* 5.5 0.4 - - - +
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Residues in contact with PRO 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA* 1.4 86.2 - - + +
17D HIS* 1.3 59.0 + - - +
19D LEU* 3.7 5.1 - - + +
20D PHE* 2.9 33.3 + - - +
80D PHE* 3.6 33.4 - - + -
105D LEU* 4.2 12.9 - - + +
106D GLU 3.9 1.8 - - - -
107D ALA* 3.4 37.0 - - + +
111D GLY 3.7 16.2 - - - +
112D SER* 4.0 10.5 - - - +
17X HIS* 5.2 2.0 - - + +
107X ALA* 4.9 0.9 - - + -
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Residues in contact with HIS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA* 2.9 27.1 + - + +
16D PRO* 1.3 79.5 - - - +
18D ARG* 1.3 71.0 + - + +
20D PHE* 4.1 2.1 - - - +
21D LYS* 3.4 23.7 + - - +
80D PHE* 4.0 10.5 - - + -
158D PHE 3.9 5.6 - - - +
159D ALA 2.3 32.6 + - - -
15X ALA* 3.6 29.1 - - + +
16X PRO* 5.9 0.4 - - - +
17X HIS* 3.8 4.0 - + - -
109X GLY 3.5 28.8 + - - +
110X GLY* 4.1 16.3 + - - -
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Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ILE* 3.6 21.9 - - + +
15D ALA* 3.0 13.9 + - - +
17D HIS* 1.3 94.4 - - + +
19D LEU* 1.3 68.7 + - - +
21D LYS* 3.5 2.3 + - - +
22D ALA* 3.0 21.5 + - - +
151D LEU* 3.2 39.3 + - + +
152D ALA* 5.1 0.6 - - - +
154D ASN 2.8 29.5 + - - -
155D PRO* 3.4 21.1 + - - +
157D VAL* 2.8 27.5 + - - +
158D PHE* 3.4 26.5 + - + +
159D ALA* 4.2 5.2 - - - +
159X ALA* 5.5 5.1 - - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER* 3.9 9.9 - - - +
14D ILE* 4.1 25.1 - - + -
15D ALA 3.2 6.5 + - - +
16D PRO 3.3 5.6 + - - +
18D ARG* 1.3 77.5 - - - +
20D PHE* 1.3 55.8 + - - +
22D ALA* 2.6 27.9 + - - -
23D LEU* 2.9 36.2 + - + -
105D LEU* 4.0 9.0 - - + -
112D SER* 3.7 20.0 - - - +
144D TYR* 4.8 9.0 - - + -
147D VAL* 5.2 3.4 - - + -
148D GLU* 5.5 3.1 - - - -
151D LEU* 4.5 9.0 - - + -
202D 2AN 3.2 37.5 - - + -
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PRO 2.9 18.0 + - - +
17D HIS* 4.6 2.2 - - - +
19D LEU* 1.3 75.5 - - - +
21D LYS* 1.3 56.1 + - - +
24D VAL* 3.1 39.4 - - + +
25D LEU* 3.1 41.4 + - + +
75D ILE* 4.7 3.1 - - + -
77D ALA* 3.7 32.8 - - + -
80D PHE* 3.5 37.9 - + + -
81D TYR 3.1 33.0 - - - -
82D CYS* 3.8 10.3 - - + -
103D VAL* 4.1 3.1 - - + -
105D LEU* 3.6 17.7 - - + -
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Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D HIS 3.4 19.9 + - - +
18D ARG 3.8 3.1 - - - +
19D LEU 3.1 0.6 - - - -
20D PHE* 1.3 79.5 - - - +
22D ALA* 1.3 55.6 + - - +
23D LEU 3.5 0.2 - - - -
25D LEU* 4.0 29.8 - - + +
26D GLU* 2.7 58.1 + - + +
158D PHE* 4.2 30.1 - - + +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG 3.0 15.7 + - - +
19D LEU* 2.6 10.8 + - - +
21D LYS* 1.3 72.8 - - - +
23D LEU* 1.3 58.2 + - + +
24D VAL 3.6 0.2 - - - -
26D GLU 3.8 1.2 - - - -
27D ARG* 3.3 20.3 + - - -
30D VAL* 3.9 15.7 - - + +
143D PHE* 4.3 3.8 - - - -
147D VAL* 3.7 28.0 - - + -
151D LEU* 4.2 6.3 - - + -
158D PHE* 3.8 21.9 - - + -
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 2.9 37.9 + - + +
20D PHE* 5.1 0.2 - - - -
22D ALA* 1.3 77.5 - - + +
24D VAL* 1.3 63.9 + - + +
27D ARG* 2.9 41.5 + - - +
84D TYR* 4.3 1.4 + - - -
105D LEU* 5.7 0.4 - - + -
143D PHE* 3.8 22.9 - - + -
144D TYR* 4.0 25.1 - - + +
147D VAL* 4.1 16.4 - - + -
202D 2AN 3.5 50.5 - - + +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.1 44.1 + - + +
22D ALA 3.6 0.4 - - - -
23D LEU* 1.3 85.2 - - + +
25D LEU* 1.3 70.6 + - + +
26D GLU 3.5 0.9 - - - -
27D ARG* 3.9 11.7 + - - +
28D HIS* 5.3 0.5 + - - -
72D PHE* 4.0 15.9 - - + -
82D CYS* 3.3 39.0 - - + -
84D TYR* 4.6 9.7 - - + -
103D VAL* 3.8 23.8 - - + -
202D 2AN 4.3 4.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il